JBR Genome Browser

Status: Active

We propose a novel semi-supervised approach to peak calling.

Fast and effective semi-supervised peaks analyzer SPAN Peak Analyzer is a multipurpose peak caller capable processing both conventional and ULI-Chip-seq tracks. In the semi-supervised approach, user annotates a handful of locations as peaks, valleys or peak shores, and then uses these annotations to train the model that is optimal for a given sample.

One of the major challenges of the semi-supervised learning is the procedural complexity of the manual annotation of the data, which often leads to the inaccuracies and mix-ups. We created a brand new visualization tool that would support classical genome browser capabilities and provide readily accessible integrated peak annotation and peak calling capabilities. JBR Genome Browser allows researchers to upload tracks of the Chip-seq data and perform on-the-fly annotation and peak calling for a given annotation, where results of the peak calling are immediately visualized as BED files in the same session. It can serve not only as an efficient semi-supervised peak calling engine but also as a next-generation genome browser. It provides enhanced capabilities for viewing large files, observing multiple locations simultaneously, and gathering track statistics.

Main features:

  • Supports semi-supervised peak calling with SPAN Peak Analyzer
  • Support for common track formats, e.g. WIG, BED, etc.
  • Capable to open saved IGV sessions
  • Support for combining tracks, i.e. arithmetic operations
  • Easy visualization of multiple genomic regions
  • Custom statistics tracks for multiple regions
  • Frontend-agnostic, can be used as a desktop application and web-service

More information is available here.